Indoctrination Theory

According to a lot of fans of the Mass Effect series, a popular theory about the ending of the 3rd game is that Shepard was actually indoctrinated. This would mean that the battle taking place after entering the Citadel at the end of the game is actually taking place in his or her mind. Many of the novels focus on indoctrination going into great detail about the process and how it affects an individual. It was also a large theme of the first and second game.

The above video explains in great detail one fans theory about the ending of the game and what could have happened.